From 8ef96c9ca76cb1b088347bc4e51948359f9fa7cc Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 16 Jan 2026 17:24:00 +0100
Subject: [PATCH] DAQ: Doesn't work and don't know why

---
 src/aare/common/autofocus_tools.py |  5 +++++
 src/aare/daq/daq.py                | 12 ++++--------
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/aare/common/autofocus_tools.py b/src/aare/common/autofocus_tools.py
index 25056e21..66747022 100644
--- a/src/aare/common/autofocus_tools.py
+++ b/src/aare/common/autofocus_tools.py
@@ -16,9 +16,14 @@ def focus_measure_edges(gray: np.ndarray, mask: np.ndarray | None = None) -> flo
     # threshold relative to median -> knocks out noise floor
     t = float(np.median(roi) * 3.0)
     strong = roi[roi > t]
+
     if strong.size == 0:
         return 0.0
 
+    print(f"mask pixels: {mask.sum()}, "
+          f"focus={strong.mean():.2f}"
+          f"strong_size={strong.size}")
+
     return float(strong.mean())  # higher = sharper
 
 def focus_measure_blob_size(gray: np.ndarray, mask: np.ndarray | None = None) -> float:
diff --git a/src/aare/daq/daq.py b/src/aare/daq/daq.py
index a1745fed..61fcae0d 100644
--- a/src/aare/daq/daq.py
+++ b/src/aare/daq/daq.py
@@ -408,11 +408,8 @@ class AareDAQ:
             time.sleep(settle_time_s)
 
             # Capture image
-            img = self.camera_image
-            img = img[:, ::-1, :].copy()  # Apply horizontal flip to match GUI
-            gray = cv2.cvtColor(img, cv2.COLOR_RGB2GRAY)
+            gray = self.camera_image_gray
 
-            print(gray.shape)
             if gray is None:
                 logger.warning(f"Failed to get image at z={z_pos:.4f}")
                 continue
@@ -423,13 +420,12 @@ class AareDAQ:
                 y, x = np.ogrid[:h, :w]
                 focus_mask = (x - center_x) ** 2 + (y - center_y) ** 2 <= radius_pxl ** 2
 
+            print(focus_mask.shape)
+            print(gray.shape)
+
             # Calculate focus measure
             fm = focus_measure_edges(gray, focus_mask)
 
-            roi_pixels = gray[focus_mask] if focus_mask is not None else gray.ravel()[:2824]
-            print(f"Step {i}: gray mean={gray.mean():.1f}, roi mean={roi_pixels.mean():.1f}, "
-                  f"roi std={roi_pixels.std():.1f}, roi min={roi_pixels.min()}, roi max={roi_pixels.max()}")
-
             z_positions.append(z_pos)
             focus_values.append(fm)
             logger.debug(f"Autofocus step {i + 1}/{n_steps}: z={z_pos:.4f}mm, focus={fm:.2f}")